On Fri, May 6, 2016 at 4:43 PM, Yong Wang <wyongciac.gmail.com> wrote:
> Hi,
>
> I want to titrate a ligand in complex with a protein. By following the
> section of "Extending constant pH to additional titratable groups" in
> Amber15 manual, I tried to prepare the parameters for Amber14. Now I
> already got the reference pKa, partial charges and reference energy (using
> TI). Then I added the parameters to the file of
> $AMBERHOME/AmberTools/src/etc/cpinutils/residues.py.
>
You need to edit
$AMBERHOME/AmberTools/src/parmed/parmed/amber/titratable_residues.py
instead (for AmberTools 16 -- for AmberTools 15, the correct file is
chemistry/amber/titratable_residues.py).
But I suggest upgrading to AmberTools 16, especially if you are having
trouble (as that is the version that gets the best support).
>
> But I encountered a problem with cpinutil.py (python
> ~/software/amber14/bin/cpinutil.py
> --describe) to prepare the cpin file. The errors are pasted as below:
>
> Traceback (most recent call last):
>
> File "amber14/bin/cpinutil.py", line 11, in <module>
>
> from chemistry.amber import titratable_residues as residues
>
> File
>
> "amber14/lib/python2.7/site-packages/chemistry/amber/titratable_residues.py",
> line 853
>
> XXX = TitratableResidue('XXX', ['C13','H1', 'C17','H2', 'H3',
> 'C02','N01','H4',
>
> ^
> SyntaxError: invalid syntax
>
This is a Python code, and as such, modifying it requires some experience
coding and debugging Python. A SyntaxError in Python typically means
you've made a typo -- a missing parentheses, quotation mark, comma, etc.
Look for some kind of trivial typo near the marker.
HTH,
Jason
--
Jason M. Swails
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Received on Fri May 06 2016 - 15:30:03 PDT
